The Rev 2 PCB arrived this afternoon, but the Rev 3 design was started a few hours later....
Reviewing the AD5242 datasheet shows the wiper/leg voltages need to be within the supply voltage range. The current design has the digital pots powered from 3.3v rail to avoid level shifting the i2c bus. But the Atari needs 5v to the digital pot. I removed the 1M AD5242 chip, mounted it on a breakout board, and tested operation in bread board. Test circuit with the digital pot setup with another resistor as a voltage divider resulted in the observed behavior. Works when powered from 5V, When powered by 3.3V with 5V to the digital pot, no good.
So Rev 3 will power all of the i2c chips with +5V and still have one bus with level shifters for the ESP.
Digikey has the AD5242 1M back in stock but the price is up to $4.24 each for 1-9 pcs.